Re: Fixing COM of one atom in selection and letting the other move

From: Vermaas, Joshua (
Date: Thu Feb 16 2017 - 10:58:32 CST

I mean, you *could* add position restraints or constraints with the appropriate NAMD flags, and it might be preferable, since that sort of constraint incurs less overhead since it can be evaluated locally. Just don't do both, since then the effective force constant is the sum of the two, which is not what you expect.

On 02/15/2017 03:24 PM, Life Sciences Inc wrote:
I have checked the com distance between both phosphate of lipids and CA atoms of protein in my output file from colvars and apparently the com of CA is getting closer to the phosphate atoms but do I have to fix any of the atoms by changing the B column in my pdb e.g fixing phosphate atoms , which I have already fixed in my code with dummy atom parameter? If not then it means the input which I made is correct ....

On Wed, Feb 15, 2017 at 1:12 AM, Vermaas, Joshua <<>> wrote:
The distance Z colvar is relative. So the position of main along the z axis relative to ref. If your dummy is where you want it to be, you indeed give 0.

Josh Vermaas

Director's Postdoctoral Fellow
National Renewable Energy Laboratory<><<>>

On Feb 14, 2017, at 11:15 AM, Life Sciences Inc <<><<>>> wrote:

Hi all

I am trying to fix the center of mass of one of my selection in lipid bilayer say phosphate atoms, and my protein which is inserted inside the lipid bilayer in z direction, I want the com of protein selection and lipid bilayer selection to be exactly the same after equilibration of my system, for this purpose I have used colvars , can anyone tell me am I going in the right direction my input for colvar is as follows and also let me know if I am giving 0.0 with centers parameter my protein selection will be at 0 with respect to lipid selection or do I have to give the 7.218 for centers value?

colvarsTrajFrequency 100

colvar {
  name d

  width 1.0 # typical displacement is set to 1 Angstrom

  distanceZ {
    ref {
      dummyAtom (0.076, 0.416, 7.218) # fixed position for ref atoms from bilayer
    main {

      # group definition: selection of the protein, which I need to move towards the com of the ref selection
      psfSegID P1
      atomNameResidueRange CA 1-12


harmonic { # Define a moving harmonic restraint
  colvars d # acting on 1 colvars

  centers 0.0 #
  forceConstant 10.0 # unit is kcal/mol/[width]^2


Thanks in advance

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:04 CST